Exposure of DNA to carcinogens, radiation, oxidation agents or other agents can damage base pairs. Such damage can ultimately lead to cell apoptosis or tumor growth. Detection and diagnosis of such damage could potentially lead to treatments and/or preventative measures. However, methods for detecting such damage are limited. Conventional methods for detecting specific DNA damage include: (I) DNA digestion followed by LC-MS analysis and (2) gel electrophoretic analysis of primer extension studies. The first method is widely employed but requires substantial chemical and enzymatic manipulation that may introduce artifacts. In addition, no sequence information is gained, and the sensitivity is limited. In the second method, the sequence of the area of the genome of interest must already be known, and the sensitivity is also limited. A third method for assessing global DNA damage is the “comet assay”. Although widely employed to analyze generic DNA damage, it does not provide any information on either the type or location of the lesions.